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| author | Alexander Kabui | 2021-12-01 10:03:03 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2021-12-10 09:58:29 +0300 |
| commit | 7b63fb20154801d658150fcb41262a7c9f108183 (patch) | |
| tree | f6533f60d417bd3244eacf7d79f18404947f57e2 /gn3/computations | |
| parent | 3e22ff2d9f21316060893d47f0b014bdaf4ab359 (diff) | |
| download | genenetwork3-7b63fb20154801d658150fcb41262a7c9f108183.tar.gz | |
minor pr fixes
Diffstat (limited to 'gn3/computations')
| -rw-r--r-- | gn3/computations/correlations.py | 15 |
1 files changed, 11 insertions, 4 deletions
diff --git a/gn3/computations/correlations.py b/gn3/computations/correlations.py index 15ee1fa..d95ecee 100644 --- a/gn3/computations/correlations.py +++ b/gn3/computations/correlations.py @@ -132,9 +132,16 @@ def fast_compute_all_sample_correlation(this_trait, for target_trait in target_dataset: trait_name = target_trait.get("trait_id") target_trait_data = target_trait["trait_sample_data"] - processed_values.append((trait_name, corr_method, - list(zip(*list(filter_shared_sample_keys( - this_trait_samples, target_trait_data)))))) + + try: + this_vals, target_vals = list(zip(*list(filter_shared_sample_keys( + this_trait_samples, target_trait_data)))) + + processed_values.append( + (trait_name, corr_method, this_vals, target_vals)) + except ValueError: + continue + with closing(multiprocessing.Pool()) as pool: results = pool.starmap(compute_sample_r_correlation, processed_values) @@ -173,7 +180,7 @@ def compute_all_sample_correlation(this_trait, except ValueError: # case where no matching strain names - this_vals, target_vals = [] + continue sample_correlation = compute_sample_r_correlation( trait_name=trait_name, |